The attacking midfielder made it five goals in four games when broke the deadlock in the second-half. Leon Bailey, linked recently with Manchester City, showed quick feet in the box and spotted the overlapping run of Havertz.
Despite coming under pressure from two defenders, the youngster managed to prod the ball through the smallest of gaps between the legs of goalkeeper Alexander Schwolow to hand Leverkusen the lead 10 minutes after the interval.
But in a huge blow to Leverkusen's chances of securing Champions League qualification, Havertz's night came to a premature conclusion when was forced off with injury after tangling with Freiburg defender Christian Gunter.
The 20-year-old could have no complaints about the tackle - a fair, 50-50 test of strength with a shoulder barge - and the referee was correct in awarding a throw-in, not a free-kick.
But Havertz's leg appeared to get trapped in turf as he was bundled over and that will cause some concern for the Leverkusen coaching staff as he was replaced by Moussa Diaby after 65 minutes.